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Sánchez IE, Galpern EA, Ferreiro DU. Solvent constraints for biopolymer folding and evolution in extraterrestrial environments. Proc Natl Acad Sci U S A 2024; 121:e2318905121. [PMID: 38739787 PMCID: PMC11127021 DOI: 10.1073/pnas.2318905121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
We propose that spontaneous folding and molecular evolution of biopolymers are two universal aspects that must concur for life to happen. These aspects are fundamentally related to the chemical composition of biopolymers and crucially depend on the solvent in which they are embedded. We show that molecular information theory and energy landscape theory allow us to explore the limits that solvents impose on biopolymer existence. We consider 54 solvents, including water, alcohols, hydrocarbons, halogenated solvents, aromatic solvents, and low molecular weight substances made up of elements abundant in the universe, which may potentially take part in alternative biochemistries. We find that along with water, there are many solvents for which the liquid regime is compatible with biopolymer folding and evolution. We present a ranking of the solvents in terms of biopolymer compatibility. Many of these solvents have been found in molecular clouds or may be expected to occur in extrasolar planets.
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Affiliation(s)
- Ignacio E. Sánchez
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos AiresCP1428, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Buenos AiresCP1428, Argentina
| | - Ezequiel A. Galpern
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos AiresCP1428, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Buenos AiresCP1428, Argentina
| | - Diego U. Ferreiro
- Laboratorio de Fisiología de Proteínas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos AiresCP1428, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Buenos AiresCP1428, Argentina
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2
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Sarkar R, Mainan A, Roy S. Influence of ion and hydration atmospheres on RNA structure and dynamics: insights from advanced theoretical and computational methods. Chem Commun (Camb) 2024. [PMID: 38501190 DOI: 10.1039/d3cc06105a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
RNA, a highly charged biopolymer composed of negatively charged phosphate groups, defies electrostatic repulsion to adopt well-defined, compact structures. Hence, the presence of positively charged metal ions is crucial not only for RNA's charge neutralization, but they also coherently decorate the ion atmosphere of RNA to stabilize its compact fold. This feature article elucidates various modes of close RNA-ion interactions, with a special emphasis on Mg2+ as an outer-sphere and inner-sphere ion. Through examples, we highlight how inner-sphere chelated Mg2+ stabilizes RNA pseudoknots, while outer-sphere ions can also exert long-range electrostatic interactions, inducing groove narrowing, coaxial helical stacking, and RNA ring formation. In addition to investigating the RNA's ion environment, we note that the RNA's hydration environment is relatively underexplored. Our study delves into its profound interplay with the structural dynamics of RNA, employing state-of-the-art atomistic simulation techniques. Through examples, we illustrate how specific ions and water molecules are associated with RNA functions, leveraging atomistic simulations to identify preferential ion binding and hydration sites. However, understanding their impact(s) on the RNA structure remains challenging due to the involvement of large length and long time scales associated with RNA's dynamic nature. Nevertheless, our contributions and recent advances in coarse-grained simulation techniques offer insights into large-scale structural changes dynamically linked to the RNA ion atmosphere. In this connection, we also review how different cutting-edge computational simulation methods provide a microscopic lens into the influence of ions and hydration on RNA structure and dynamics, elucidating distinct ion atmospheric components and specific hydration layers and their individual and collective impacts.
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Affiliation(s)
- Raju Sarkar
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India.
| | - Avijit Mainan
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India.
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India.
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3
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Lorenz-Ochoa KA, Baiz CR. Ultrafast Spectroscopy Reveals Slow Water Dynamics in Biocondensates. J Am Chem Soc 2023; 145:27800-27809. [PMID: 38061016 DOI: 10.1021/jacs.3c10862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Cells achieve high spatiotemporal control over biochemical processes through compartmentalization to membrane-bound as well as membraneless organelles that assemble by liquid-liquid phase separation. Characterizing the balance of forces within these environments is essential to understanding their stability and function, and water is an integral part of the condensate, playing an important role in mediating electrostatic and hydrogen-bonding interactions. Here, we investigate the ultrafast, picosecond hydrogen-bond dynamics of a model biocondensate consisting of a peptide poly-l-arginine (Poly-R) and the nucleic acid adenosine monophosphate (AMP) using coherent two-dimensional infrared (2D IR) spectroscopy. We investigated three vibrational modes: the arginine side-chain C═N stretches, an AMP ring mode, and the amide backbone carbonyl stretching modes. Dynamics slow considerably between the dilute phase and the condensate phase for each vibrational probe. For example, the arginine side-chain C═N modes slow from 0.38 to 2.26 ps due to strong electrostatic interactions. All-atom molecular dynamics simulations provide an atomistic interpretation of the H-bond network disruption resulting from electrostatic contributions as well as collapse within the condensate. Simulations predict that a fraction of water molecules are highly constrained within the condensate, explaining the observed slowdown in the H-bond dynamics.
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Affiliation(s)
- Keegan A Lorenz-Ochoa
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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4
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Sarkar R, Singh RK, Roy S. Hierarchical Hydration Dynamics of RNA with Nano-Water-Pool at Its Core. J Phys Chem B 2023; 127:6903-6919. [PMID: 37506269 DOI: 10.1021/acs.jpcb.3c03553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Many functional RNAs fold into a compact, roughly globular shape by minimizing the electrostatic repulsion between their negatively charged phosphodiester backbone. The fold of such close, compact RNA architecture is often so designed that its outer surface and complex core both are predominately populated by phosphate groups loosely sequestering bases in the intermediate layers. A number of helical junctions maintain the RNA core and its nano-water-pool. While the folding of RNA is manifested by its counterion environment composed of mixed mono- and divalent salts, the concerted role of ion and water in maintaining an RNA fold is yet to be explored. In this work, detailed atomistic simulations of SAM-I and Add Adenine riboswitch aptamers, and subgenomic flavivirus RNA (sfRNA) have been performed in a physiological mixed mono- and divalent salt environment. All three RNA systems have compact folds with a core diameter of range 1-1.7 nm. The spatiotemporal heterogeneity of RNA hydration was probed in a layer-wise manner by distinguishing the core, the intermediate, and the outer layers. The layer-wise decomposition of hydrogen bonds and collective single-particle reorientational dynamics reveal a nonmonotonic relaxation pattern with the slowest relaxation observed at the intermediate layers that involves functionally important tertiary motifs. The slowness of this intermediate layer is attributed to two types of long-resident water molecules: (i) water from ion-hydration layers and (ii) structurally trapped water (distant from ions). The relaxation kinetics of the core and the surface water essentially exposed to the phosphate groups show well-separated time scales from the intermediate layers. In the slow intermediate layers, site-specific ions and water control the functional dynamics of important RNA motifs like kink-turn, observed in different structure-probing experiments. Most interestingly, we find that as the size of the RNA core increases (SAM1 core < sfRNAcore < Add adenine core), its hydration tends to show faster relaxation. The hierarchical hydration and the layer-wise base-phosphate composition uniquely portray the globular RNA to act like a soft vesicle with a quasi-dynamic nano-water-pool at its core.
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Affiliation(s)
- Raju Sarkar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Rishabh K Singh
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
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5
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Bin M, Reiser M, Filianina M, Berkowicz S, Das S, Timmermann S, Roseker W, Bauer R, Öström J, Karina A, Amann-Winkel K, Ladd-Parada M, Westermeier F, Sprung M, Möller J, Lehmkühler F, Gutt C, Perakis F. Coherent X-ray Scattering Reveals Nanoscale Fluctuations in Hydrated Proteins. J Phys Chem B 2023. [PMID: 37209106 DOI: 10.1021/acs.jpcb.3c02492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Hydrated proteins undergo a transition in the deeply supercooled regime, which is attributed to rapid changes in hydration water and protein structural dynamics. Here, we investigate the nanoscale stress-relaxation in hydrated lysozyme proteins stimulated and probed by X-ray Photon Correlation Spectroscopy (XPCS). This approach allows us to access the nanoscale dynamics in the deeply supercooled regime (T = 180 K), which is typically not accessible through equilibrium methods. The observed stimulated dynamic response is attributed to collective stress-relaxation as the system transitions from a jammed granular state to an elastically driven regime. The relaxation time constants exhibit Arrhenius temperature dependence upon cooling with a minimum in the Kohlrausch-Williams-Watts exponent at T = 227 K. The observed minimum is attributed to an increase in dynamical heterogeneity, which coincides with enhanced fluctuations observed in the two-time correlation functions and a maximum in the dynamic susceptibility quantified by the normalized variance χT. The amplification of fluctuations is consistent with previous studies of hydrated proteins, which indicate the key role of density and enthalpy fluctuations in hydration water. Our study provides new insights into X-ray stimulated stress-relaxation and the underlying mechanisms behind spatiotemporal fluctuations in biological granular materials.
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Affiliation(s)
- Maddalena Bin
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Mario Reiser
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Mariia Filianina
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Sharon Berkowicz
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Sudipta Das
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Sonja Timmermann
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072 Siegen, Germany
| | - Wojciech Roseker
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Robert Bauer
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
- Freiberg Water Research Center, Technische Universität Bergakademie Freiberg, 09599 Freiberg, Germany
| | - Jonatan Öström
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Aigerim Karina
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Katrin Amann-Winkel
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute of Physics, Johannes Gutenberg University, 55128 Mainz, Germany
| | - Marjorie Ladd-Parada
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Fabian Westermeier
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Johannes Möller
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Felix Lehmkühler
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Christian Gutt
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072 Siegen, Germany
| | - Fivos Perakis
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
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6
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Sogabe T, Nakagawa H, Yamada T, Koseki S, Kawai K. Effect of water activity on the mechanical glass transition and dynamical transition of bacteria. Biophys J 2022; 121:3874-3882. [PMID: 36057786 PMCID: PMC9674979 DOI: 10.1016/j.bpj.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 08/01/2022] [Accepted: 08/31/2022] [Indexed: 11/30/2022] Open
Abstract
The purpose of this study was to clarify the glass-transition behavior of bacteria (Cronobacter sakazakii) as a function of water activity (aw). From the water sorption isotherm (298 K) for C. sakazakii, monolayer water content and monolayer aw were determined to be 0.0724 g/g-dry matter and 0.252, respectively. Mechanical relaxation was investigated at 298 K. In a higher aw range of over 0.529, the degree of mechanical relaxation increased with an increase in aw. From the effect of aw on the degree of mechanical relaxation, the mechanical awc (aw at which mechanical glass transition occurs at 298 K) was determined to be 0.667. Mean-square displacement of atoms in the bacteria was investigated by incoherent elastic neutron scattering. The mean-square displacement increased gradually with an increase in temperature depending on the aw of samples. From the linear fitting, two or three dynamical transition temperatures (low, middle, and high Tds) were determined at each aw. The low-Td values (142-158 K) were almost independent from aw. There was a minor effect of aw on the middle Td (214-234 K) except for the anhydrous sample (261 K). The high Td (252-322 K) largely increased with the decrease in aw. From the aw dependence of the high Td, the dynamical awc was determined to be 0.675, which was almost equivalent to the mechanical awc. The high Td was assumed to be the glass-transition temperature (Tg), and anhydrous Tg was estimated to be 409 K. In addition, molecular relaxation time (τ) of the bacteria was calculated as a function of aw. From the result, it is suggested that the progress of metabolism in the bacterial system requires a lower τ than approximately 6 × 10-5 s.
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Affiliation(s)
- Tomochika Sogabe
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Hiroshi Nakagawa
- Materials Sciences Research Center, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan; J-PARC Center, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan
| | - Takeshi Yamada
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), Tokai, Ibaraki, Japan
| | - Shigenobu Koseki
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Kiyoshi Kawai
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.
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7
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Pena-Francesch A, Jung H, Tyagi M, Demirel MC. Diffusive Dynamic Modes of Recombinant Squid Ring Teeth Proteins by Neutron Spectroscopy. Biomacromolecules 2022; 23:3165-3173. [PMID: 35767422 DOI: 10.1021/acs.biomac.2c00266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Stimuli-responsive structural proteins are emerging as promising biocompatible materials for a wide range of biological and nonbiological applications. To understand the physical properties of structural proteins and to replicate their performance in biosynthetic systems, there is a need to understand the molecular mechanisms and relationships that regulate their structure, dynamics, and properties. Here, we study the dynamics of a recombinant squid-inspired protein from Loligo vulgaris (Lv18) by elastic and quasielastic neutron scattering (QENS) to understand the connection between nanostructure, chain dynamics, and mechanical properties. Lv18 is a semicrystalline structural protein, which is plasticized by water above its glass transition temperature at 35 °C. Elastic scans revealed an increased protein chain mobility upon hydration, superimposed dynamic processes, and a decrease in dynamic transition temperatures. Further analysis by QENS revealed that while dry Lv18 protein dynamics are dominated by localized methyl group rotations, hydrated Lv18 dynamics are dominated by the confined diffusion of flexible chains within a β-sheet nanocrystalline network (8 Å of confinement radius). Our findings establish a relationship between the segment block architecture of Lv18, the diffusive motions within the protein structure, and the mechanical properties of recombinant squid proteins, which will advance the molecular design of novel high-performance protein-inspired materials with tailored dynamics and mechanical properties.
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Affiliation(s)
- Abdon Pena-Francesch
- Department of Materials Science and Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Huihun Jung
- Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, Gaithersburg, Maryland 20899, United States.,Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Melik C Demirel
- Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Materials Research Institute, and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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8
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Rosi BP, D’Angelo A, Buratti E, Zanatta M, Tavagnacco L, Natali F, Zamponi M, Noferini D, Corezzi S, Zaccarelli E, Comez L, Sacchetti F, Paciaroni A, Petrillo C, Orecchini A. Impact of the Environment on the PNIPAM Dynamical Transition Probed by Elastic Neutron Scattering. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benedetta P. Rosi
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Arianna D’Angelo
- Laboratoire de Physique des Solides, CNRS, Université Paris-Saclay, 510 Rue André Rivière, 91405 Orsay, France
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, Cedex 9, France
| | - Elena Buratti
- Dipartimento di Fisica, CNR-ISC c/o Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Marco Zanatta
- Dipartimento di Fisica, Università di Trento, via Sommarive 14, 38123 Trento, Italy
| | - Letizia Tavagnacco
- Dipartimento di Fisica, CNR-ISC c/o Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Francesca Natali
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, Cedex 9, France
- CNR-IOM, OGG, 71 Avenue des Martyrs, 38043 Grenoble, Cedex 9, France
| | - Michaela Zamponi
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Daria Noferini
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, 85747 Garching, Germany
- European Spallation Source ERIC, Box 176, 221 00 Lund, Sweden
| | - Silvia Corezzi
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Emanuela Zaccarelli
- Dipartimento di Fisica, CNR-ISC c/o Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Lucia Comez
- Dipartimento di Fisica e Geologia, CNR-IOM c/o Università di Perugia, via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesco Sacchetti
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Alessandro Paciaroni
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Caterina Petrillo
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Andrea Orecchini
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Dipartimento di Fisica e Geologia, CNR-IOM c/o Università di Perugia, via Alessandro Pascoli, 06123 Perugia, Italy
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9
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Zheng L, Liu Z, Zhang Q, Li S, Huang J, Zhang L, Zan B, Tyagi M, Cheng H, Zuo T, Sakai VG, Yamada T, Yang C, Tan P, Jiang F, Chen H, Zhuang W, Hong L. Universal dynamical onset in water at distinct material interfaces. Chem Sci 2022; 13:4341-4351. [PMID: 35509458 PMCID: PMC9006901 DOI: 10.1039/d1sc04650k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 03/18/2022] [Indexed: 12/13/2022] Open
Abstract
Interfacial water remains liquid and mobile much below 0 °C, imparting flexibility to the encapsulated materials to ensure their diverse functions at subzero temperatures. However, a united picture that can describe the dynamical differences of interfacial water on different materials and its role in imparting system-specific flexibility to distinct materials is lacking. By combining neutron spectroscopy and isotope labeling, we explored the dynamics of water and the underlying substrates independently below 0 °C across a broad range of materials. Surprisingly, while the function-related anharmonic dynamical onset in the materials exhibits diverse activation temperatures, the surface water presents a universal onset at a common temperature. Further analysis of the neutron experiment and simulation results revealed that the universal onset of water results from an intrinsic surface-independent relaxation: switching of hydrogen bonds between neighboring water molecules with a common energy barrier of ∼35 kJ mol−1. We demonstrated that the dynamical onset of interfacial water is an intrinsic property of water itself, resulting from a surface independent relaxation process in water with an approximately universal energy barrier of ∼35 kJ mol−1.![]()
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Affiliation(s)
- Lirong Zheng
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35000, China
| | - Zhuo Liu
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Zhang
- College of Chemistry and Materials Science, Inner Mongolia University for Nationalities, Tongliao, Inner Mongolia 028043, China
| | - Song Li
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan Huang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Zhang
- School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bing Zan
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - He Cheng
- China Spallation Neutron Source (CSNS), Institute of High Energy Physics (IHEP), Chinese Academy of Science (CAS), Dongguan 523803, China
- Dongguan Institute of Neutron Science (DINS), Dongguan 523808, China
| | - Taisen Zuo
- China Spallation Neutron Source (CSNS), Institute of High Energy Physics (IHEP), Chinese Academy of Science (CAS), Dongguan 523803, China
- Dongguan Institute of Neutron Science (DINS), Dongguan 523808, China
| | - Victoria García Sakai
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Science & Technology Facilities Council, Didcot OX11 0QX, UK
| | - Takeshi Yamada
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society, 162-1 Shirakata, Tokai, Naka, Ibaraki 319-1106, Japan
| | - Chenxing Yang
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Pan Tan
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan Jiang
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35000, China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35000, China
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China
| | - Liang Hong
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
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10
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Mamontov E, Cheng Y, Daemen LL, Keum JK, Kolesnikov AI, Pajerowski D, Podlesnyak A, Ramirez-Cuesta AJ, Ryder MR, Stone MB. Effect of Hydration on the Molecular Dynamics of Hydroxychloroquine Sulfate. ACS OMEGA 2020; 5:21231-21240. [PMID: 32869009 PMCID: PMC7423024 DOI: 10.1021/acsomega.0c03091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 07/24/2020] [Indexed: 06/11/2023]
Abstract
Chloroquine and its derivative hydroxychloroquine are primarily known as antimalaria drugs. Here, we investigate the influence of hydration water on the molecular dynamics in hydroxychloroquine sulfate, a commonly used solubilized drug form. When hydration, even at a low level, results in a disordered structure, as opposed to the highly ordered structure of dry hydroxychloroquine sulfate, the activation barriers for the rotation of methyl groups in the drug molecules become randomized and, on average, significantly reduced. The facilitated stochastic motions of the methyl groups may benefit the biomolecular activity due to the more efficient sampling of the energy landscape in the disordered hydration environment experienced by the drug molecules in vivo.
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11
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Kämpf K, Demuth D, Zamponi M, Wuttke J, Vogel M. Quasielastic neutron scattering studies on couplings of protein and water dynamics in hydrated elastin. J Chem Phys 2020; 152:245101. [PMID: 32610976 DOI: 10.1063/5.0011107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Performing quasielastic neutron scattering measurements and analyzing both elastic and quasielasic contributions, we study protein and water dynamics of hydrated elastin. At low temperatures, hydration-independent methyl group rotation dominates the findings. It is characterized by a Gaussian distribution of activation energies centered at about Em = 0.17 eV. At ∼195 K, coupled protein-water motion sets in. The hydration water shows diffusive motion, which is described by a Gaussian distribution of activation energies with Em = 0.57 eV. This Arrhenius behavior of water diffusion is consistent with previous results for water reorientation, but at variance with a fragile-to-strong crossover at ∼225 K. The hydration-related elastin backbone motion is localized and can be attributed to the cage rattling motion. We speculate that its onset at ∼195 K is related to a secondary glass transition, which occurs when a β relaxation of the protein has a correlation time of τβ ∼ 100 s. Moreover, we show that its temperature-dependent amplitude has a crossover at the regular glass transition Tg = 320 K of hydrated elastin, where the α relaxation of the protein obeys τα ∼ 100 s. By contrast, we do not observe a protein dynamical transition when water dynamics enters the experimental time window at ∼240 K.
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Affiliation(s)
- Kerstin Kämpf
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstraße 6, 64289 Darmstadt, Germany
| | - Dominik Demuth
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstraße 6, 64289 Darmstadt, Germany
| | - Michaela Zamponi
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Lichtenbergstraße 1, 85747 Garching, Germany
| | - Joachim Wuttke
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Lichtenbergstraße 1, 85747 Garching, Germany
| | - Michael Vogel
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstraße 6, 64289 Darmstadt, Germany
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12
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Krah A, Huber RG, Bond PJ. How Ligand Binding Affects the Dynamical Transition Temperature in Proteins. Chemphyschem 2020; 21:916-926. [DOI: 10.1002/cphc.201901221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/03/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Alexander Krah
- School of Computational SciencesKorea Institute for Advanced Study 85 Hoegiro, Dongdaemun-gu Seoul 02455 Republic of Korea
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR) 30 Biopolis Str., #07-01 Matrix 138671 Singapore
| | - Roland G. Huber
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR) 30 Biopolis Str., #07-01 Matrix 138671 Singapore
| | - Peter J. Bond
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR) 30 Biopolis Str., #07-01 Matrix 138671 Singapore
- National University of SingaporeDepartment of Biological Sciences 14 Science Drive 4 Singapore 117543
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13
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Tian B, Garcia Sakai V, Pappas C, van der Goot AJ, Bouwman WG. Fibre formation in calcium caseinate influenced by solvent isotope effect and drying method – A neutron spectroscopy study. Chem Eng Sci 2019. [DOI: 10.1016/j.ces.2019.07.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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14
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Benedetto A, Kearley GJ. Dynamics from elastic neutron-scattering via direct measurement of the running time-integral of the van Hove distribution function. Sci Rep 2019; 9:11284. [PMID: 31375739 PMCID: PMC6677729 DOI: 10.1038/s41598-019-46835-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 07/03/2019] [Indexed: 12/03/2022] Open
Abstract
We present a new neutron-scattering approach to access the van Hove distribution function directly in the time domain, I(t), which reflects the system dynamics. Currently, I(t) is essentially determined from neutron energy-exchange. Our method consists of the straightforward measurement of the running time-integral of I(t), by computing the portion of scattered neutrons corresponding to species at rest within a time t, (conceptually elastic scattering). Previous attempts failed to recognise this connection. Starting from a theoretical standpoint, a practical realisation is assessed via numerical methods and an instrument simulation.
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Affiliation(s)
- Antonio Benedetto
- School of Physics, University College Dublin, Dublin 4, Ireland. .,School of Chemistry, University College Dublin, Dublin 4, Ireland. .,Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland. .,Department of Sciences, University of Roma Tre, Rome, Italy. .,Laboratory for Neutron Scattering, Paul Scherrer Institut, Villigen, Switzerland.
| | - Gordon J Kearley
- School of Chemistry, University College Dublin, Dublin 4, Ireland
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15
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Pathak AK, Bandyopadhyay T. Temperature Induced Dynamical Transition of Biomolecules in Polarizable and Nonpolarizable TIP3P Water. J Chem Theory Comput 2019; 15:2706-2718. [PMID: 30849227 DOI: 10.1021/acs.jctc.9b00005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Temperature induced dynamical transition (DT), associated with a sharp rise in molecular flexibility, is well-known to be exhibited between 270 and 280 K in glycerol to 200-230 K in hydrated biomolecules and is controlled by diffusivity (viscosity) of the solvation layer. In the molecular dynamics (MD) community, especially for water as a solvent, this has been an intense area of research despite decades of investigations. However, in general, water in these studies is described by empirical nonpolarizable force fields in which electronic polarizability is treated implicitly with effective charges and related parameters. This might have led to the present trait of discovery that DTs of biomolecules, irrespective of the potential functions for water models used, occur within a narrow band of temperature variation (30-40 K). Whereas a water molecule in a biomolecular surface and one in bulk are polarized differently, therefore explicit treatment of water polarizability would be a powerful approach toward the treatment of hydration water, believed to cause the DT manifestation. Using MD simulations, we investigated the effects of polarizable water on the DT of biomolecules and the dynamic properties of hydration water. We chose two types of solutes: globular protein (lysozyme) and more open and flexible RNAs (a hairpin and a riboswitch) with different natures of hydrophilic sites than proteins in general. We found that the characteristic temperature of DT ( TDT) for the solutes in polarizable water is always higher than that in its nonpolarizable counterpart. In particular, for RNAs, the variations are found to be ∼45 K between the two water models, whereas for the more compact lysozyme, it is only ∼4 K. The results are discussed in light of the enormous increase in relaxation times of a liquid upon cooling in the paradigm of dynamic switchover in hydration water with liquid-liquid phase transition, derived from the existence of the second critical point. Our result supports the idea that structures of biomolecules and their interactions with the hydration water determines TDT and provides evidence for the decisive role of polarizable water on the onset of DT, which has been hitherto ignored.
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Affiliation(s)
- Arup Kumar Pathak
- Theoretical Chemistry Section , Bhabha Atomic Research Centre , Mumbai 400 085 , India.,Homi Bhabha National Institute , Mumbai 400094 , India
| | - Tusar Bandyopadhyay
- Theoretical Chemistry Section , Bhabha Atomic Research Centre , Mumbai 400 085 , India.,Homi Bhabha National Institute , Mumbai 400094 , India
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16
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Tavagnacco L, Chiessi E, Zanatta M, Orecchini A, Zaccarelli E. Water-Polymer Coupling Induces a Dynamical Transition in Microgels. J Phys Chem Lett 2019; 10:870-876. [PMID: 30735054 PMCID: PMC6416711 DOI: 10.1021/acs.jpclett.9b00190] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/08/2019] [Indexed: 06/09/2023]
Abstract
The long debated protein dynamical transition was recently found also in nonbiological macromolecules, such as poly- N-isopropylacrylamide (PNIPAM) microgels. Here, by using atomistic molecular dynamics simulations, we report a description of the molecular origin of the dynamical transition in these systems. We show that PNIPAM and water dynamics below the dynamical transition temperature T d are dominated by methyl group rotations and hydrogen bonding, respectively. By comparing with bulk water, we unambiguously identify PNIPAM-water hydrogen bonding as mainly responsible for the occurrence of the transition. The observed phenomenology thus crucially depends on the water-macromolecule coupling, being relevant to a wide class of hydrated systems, independently from the biological function.
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Affiliation(s)
- Letizia Tavagnacco
- CNR-ISC
and Department of Physics, Sapienza University
of Rome, Piazzale A.
Moro 2, 00185 Rome, Italy
| | - Ester Chiessi
- Department
of Chemical Sciences and Technologies, University
of Rome Tor Vergata, Via della Ricerca Scientica I, 00133 Rome, Italy
| | - Marco Zanatta
- Department
of Computer Science, University of Verona, Strada Le Grazie 15, 37138 Verona, Italy
| | - Andrea Orecchini
- Department
of Physics and Geology, University of Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR-IOM
c/o Department of Physics and Geology, University
of Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - Emanuela Zaccarelli
- CNR-ISC
and Department of Physics, Sapienza University
of Rome, Piazzale A.
Moro 2, 00185 Rome, Italy
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17
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Scheidt WR, Li J, Sage JT. What Can Be Learned from Nuclear Resonance Vibrational Spectroscopy: Vibrational Dynamics and Hemes. Chem Rev 2017; 117:12532-12563. [PMID: 28921972 PMCID: PMC5639469 DOI: 10.1021/acs.chemrev.7b00295] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Nuclear resonance
vibrational spectroscopy (NRVS; also known as
nuclear inelastic scattering, NIS) is a synchrotron-based method that
reveals the full spectrum of vibrational dynamics for Mössbauer
nuclei. Another major advantage, in addition to its completeness (no
arbitrary optical selection rules), is the unique selectivity of NRVS.
The basics of this recently developed technique are first introduced
with descriptions of the experimental requirements and data analysis
including the details of mode assignments. We discuss the use of NRVS
to probe 57Fe at the center of heme and heme protein derivatives
yielding the vibrational density of states for the iron. The application
to derivatives with diatomic ligands (O2, NO, CO, CN–) shows the strong capabilities of identifying mode
character. The availability of the complete vibrational spectrum of
iron allows the identification of modes not available by other techniques.
This permits the correlation of frequency with other physical properties.
A significant example is the correlation we find between the Fe–Im
stretch in six-coordinate Fe(XO) hemes and the trans Fe–N(Im)
bond distance, not possible previously. NRVS also provides uniquely
quantitative insight into the dynamics of the iron. For example, it
provides a model-independent means of characterizing the strength
of iron coordination. Prediction of the temperature-dependent mean-squared
displacement from NRVS measurements yields a vibrational “baseline”
for Fe dynamics that can be compared with results from techniques
that probe longer time scales to yield quantitative insights into
additional dynamical processes.
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Affiliation(s)
- W Robert Scheidt
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556 United States
| | - Jianfeng Li
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences , YanQi Lake, HuaiRou District, Beijing 101408, China
| | - J Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , 120 Forsyth Street, Boston, Massachusetts 02115, United States
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18
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Castellanos MM, McAuley A, Curtis JE. Investigating Structure and Dynamics of Proteins in Amorphous Phases Using Neutron Scattering. Comput Struct Biotechnol J 2016; 15:117-130. [PMID: 28138368 PMCID: PMC5257034 DOI: 10.1016/j.csbj.2016.12.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/10/2016] [Accepted: 12/13/2016] [Indexed: 02/07/2023] Open
Abstract
In order to increase shelf life and minimize aggregation during storage, many biotherapeutic drugs are formulated and stored as either frozen solutions or lyophilized powders. However, characterizing amorphous solids can be challenging with the commonly available set of biophysical measurements used for proteins in liquid solutions. Therefore, some questions remain regarding the structure of the active pharmaceutical ingredient during freezing and drying of the drug product and the molecular role of excipients. Neutron scattering is a powerful technique to study structure and dynamics of a variety of systems in both solid and liquid phases. Moreover, neutron scattering experiments can generally be correlated with theory and molecular simulations to analyze experimental data. In this article, we focus on the use of neutron techniques to address problems of biotechnological interest. We describe the use of small-angle neutron scattering to study the solution structure of biological molecules and the packing arrangement in amorphous phases, that is, frozen glasses and freeze-dried protein powders. In addition, we discuss the use of neutron spectroscopy to measure the dynamics of glassy systems at different time and length scales. Overall, we expect that the present article will guide and prompt the use of neutron scattering to provide unique insights on many of the outstanding questions in biotechnology.
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Affiliation(s)
- Maria Monica Castellanos
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, United States; Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, United States
| | - Arnold McAuley
- Department of Drug Product Development, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, United States
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, United States
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19
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Zaccai G, Natali F, Peters J, Řihová M, Zimmerman E, Ollivier J, Combet J, Maurel MC, Bashan A, Yonath A. The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering. Sci Rep 2016; 6:37138. [PMID: 27849042 PMCID: PMC5111069 DOI: 10.1038/srep37138] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/25/2016] [Indexed: 01/08/2023] Open
Abstract
Conformational changes associated with ribosome function have been identified by X-ray crystallography and cryo-electron microscopy. These methods, however, inform poorly on timescales. Neutron scattering is well adapted for direct measurements of thermal molecular dynamics, the ‘lubricant’ for the conformational fluctuations required for biological activity. The method was applied to compare water dynamics and conformational fluctuations in the 30 S and 50 S ribosomal subunits from Haloarcula marismortui, under high salt, stable conditions. Similar free and hydration water diffusion parameters are found for both subunits. With respect to the 50 S subunit, the 30 S is characterized by a softer force constant and larger mean square displacements (MSD), which would facilitate conformational adjustments required for messenger and transfer RNA binding. It has been shown previously that systems from mesophiles and extremophiles are adapted to have similar MSD under their respective physiological conditions. This suggests that the results presented are not specific to halophiles in high salt but a general property of ribosome dynamics under corresponding, active conditions. The current study opens new perspectives for neutron scattering characterization of component functional molecular dynamics within the ribosome.
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Affiliation(s)
- Giuseppe Zaccai
- Institut Laue Langevin, F-38042 Grenoble, France.,Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Francesca Natali
- Institut Laue Langevin, F-38042 Grenoble, France.,CNR-IOM, OGG, F-38042 Grenoble, France
| | - Judith Peters
- Institut Laue Langevin, F-38042 Grenoble, France.,Univ. Grenoble Alpes, LiPhy, F-38044 Grenoble, France
| | - Martina Řihová
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205- CNRS, MNHN, UPMC, EPHE UPMC, Sorbonne Universités, 57 rue Cuvier, CP 50, 75005 Paris, France.,Institute of Physics, Charles University, Faculty of Mathematics and Physics, CZ-121 16 Prague, Czech Republic
| | - Ella Zimmerman
- Weizmann Institute, Department of Structural Biology, 76100 Rehovot, Israel
| | - J Ollivier
- Institut Laue Langevin, F-38042 Grenoble, France
| | - J Combet
- Institut Laue Langevin, F-38042 Grenoble, France.,Institut Charles Sadron, CNRS-UdS, 67034 Strasbourg Cedex 2, France
| | - Marie-Christine Maurel
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205- CNRS, MNHN, UPMC, EPHE UPMC, Sorbonne Universités, 57 rue Cuvier, CP 50, 75005 Paris, France
| | - Anat Bashan
- Weizmann Institute, Department of Structural Biology, 76100 Rehovot, Israel
| | - Ada Yonath
- Weizmann Institute, Department of Structural Biology, 76100 Rehovot, Israel
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20
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Gupta M, Chakravarty C, Bandyopadhyay S. Sensitivity of Protein Glass Transition to the Choice of Water Model. J Chem Theory Comput 2016; 12:5643-5655. [DOI: 10.1021/acs.jctc.6b00825] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Madhulika Gupta
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
| | - Charusita Chakravarty
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department
of Chemistry, Indian Institute of Technology-Kharagpur, Kharagpur 721302, India
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21
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Dhindsa GK, Bhowmik D, Goswami M, O’Neill H, Mamontov E, Sumpter BG, Hong L, Ganesh P, Chu XQ. Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study. J Phys Chem B 2016; 120:10059-10068. [DOI: 10.1021/acs.jpcb.6b07511] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Gurpreet K. Dhindsa
- Department
of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
| | - Debsindhu Bhowmik
- Department
of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
| | - Monojoy Goswami
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Computer
Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hugh O’Neill
- Biology and
Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Eugene Mamontov
- Chemical
and Engineering Materials Division, Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
| | - Bobby G. Sumpter
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Computer
Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Liang Hong
- Institute of Natural Science & Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Panchapakesan Ganesh
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Xiang-qiang Chu
- Department
of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
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22
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Bellissent-Funel MC, Hassanali A, Havenith M, Henchman R, Pohl P, Sterpone F, van der Spoel D, Xu Y, Garcia AE. Water Determines the Structure and Dynamics of Proteins. Chem Rev 2016; 116:7673-97. [PMID: 27186992 DOI: 10.1021/acs.chemrev.5b00664] [Citation(s) in RCA: 505] [Impact Index Per Article: 63.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.
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Affiliation(s)
| | - Ali Hassanali
- International Center for Theoretical Physics, Condensed Matter and Statistical Physics 34151 Trieste, Italy
| | - Martina Havenith
- Ruhr-Universität Bochum , Faculty of Chemistry and Biochemistry Universitätsstraße 150 Building NC 7/72, D-44780 Bochum, Germany
| | - Richard Henchman
- Manchester Institute of Biotechnology The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Pohl
- Johannes Kepler University , Gruberstrasse, 40 4020 Linz, Austria
| | - Fabio Sterpone
- Institut de Biologie Physico-Chimique Laboratoire de Biochimie Théorique 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - David van der Spoel
- Department of Cell and Molecular Biology, Computational and Systems Biology, Uppsala University , 751 24 Uppsala, Sweden
| | - Yao Xu
- Ruhr-Universität Bochum , Faculty of Chemistry and Biochemistry Universitätsstraße 150 Building NC 7/72, D-44780 Bochum, Germany
| | - Angel E Garcia
- Center for Non Linear Studies, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
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23
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Effects of pressure on the dynamics of an oligomeric protein from deep-sea hyperthermophile. Proc Natl Acad Sci U S A 2015; 112:13886-91. [PMID: 26504206 DOI: 10.1073/pnas.1514478112] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inorganic pyrophosphatase (IPPase) from Thermococcus thioreducens is a large oligomeric protein derived from a hyperthermophilic microorganism that is found near hydrothermal vents deep under the sea, where the pressure is up to 100 MPa (1 kbar). It has attracted great interest in biophysical research because of its high activity under extreme conditions in the seabed. In this study, we use the quasielastic neutron scattering (QENS) technique to investigate the effects of pressure on the conformational flexibility and relaxation dynamics of IPPase over a wide temperature range. The β-relaxation dynamics of proteins was studied in the time ranges from 2 to 25 ps, and from 100 ps to 2 ns, using two spectrometers. Our results indicate that, under a pressure of 100 MPa, close to that of the native environment deep under the sea, IPPase displays much faster relaxation dynamics than a mesophilic model protein, hen egg white lysozyme (HEWL), at all measured temperatures, opposite to what we observed previously under ambient pressure. This contradictory observation provides evidence that the protein energy landscape is distorted by high pressure, which is significantly different for hyperthermophilic (IPPase) and mesophilic (HEWL) proteins. We further derive from our observations a schematic denaturation phase diagram together with energy landscapes for the two very different proteins, which can be used as a general picture to understand the dynamical properties of thermophilic proteins under pressure.
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24
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Sebastiani F, Longo M, Orecchini A, Comez L, De Francesco A, Muthmann M, Teixeira SCM, Petrillo C, Sacchetti F, Paciaroni A. Hydration-dependent dynamics of human telomeric oligonucleotides in the picosecond timescale: A neutron scattering study. J Chem Phys 2015; 143:015102. [DOI: 10.1063/1.4923213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- F. Sebastiani
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - M. Longo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- Elettra—Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - A. Orecchini
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - L. Comez
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - A. De Francesco
- CNR-IOM OGG c/o Institut Laue-Langevin, 71 Avenue des Martyrs, CS20156, 38042 Grenoble Cedex 9, France
| | - M. Muthmann
- Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at Heinz Maier-Leibnitz Zentrum, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - S. C. M. Teixeira
- EPSAM, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue–Langevin, 71 Avenue des Martyrs, CS20156, 38042 Grenoble Cedex 9, France
| | - C. Petrillo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - F. Sacchetti
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - A. Paciaroni
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
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25
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Khodadadi S, Sokolov AP. Protein dynamics: from rattling in a cage to structural relaxation. SOFT MATTER 2015; 11:4984-4998. [PMID: 26027652 DOI: 10.1039/c5sm00636h] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present an overview of protein dynamics based mostly on results of neutron scattering, dielectric relaxation spectroscopy and molecular dynamics simulations. We identify several major classes of protein motions on the time scale from faster than picoseconds to several microseconds, and discuss the coupling of these processes to solvent dynamics. Our analysis suggests that the microsecond backbone relaxation process might be the main structural relaxation of the protein that defines its glass transition temperature, while faster processes present some localized secondary relaxations. Based on the overview, we formulate a general picture of protein dynamics and discuss the challenges in this field.
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Affiliation(s)
- S Khodadadi
- Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
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26
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Frank AT, Zhang Q, Al-Hashimi HM, Andricioaei I. Slowdown of Interhelical Motions Induces a Glass Transition in RNA. Biophys J 2015; 108:2876-85. [PMID: 26083927 PMCID: PMC4472199 DOI: 10.1016/j.bpj.2015.04.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/21/2015] [Accepted: 04/21/2015] [Indexed: 12/29/2022] Open
Abstract
RNA function depends crucially on the details of its dynamics. The simplest RNA dynamical unit is a two-way interhelical junction. Here, for such a unit--the transactivation response RNA element--we present evidence from molecular dynamics simulations, supported by nuclear magnetic resonance relaxation experiments, for a dynamical transition near 230 K. This glass transition arises from the freezing out of collective interhelical motional modes. The motions, resolved with site-specificity, are dynamically heterogeneous and exhibit non-Arrhenius relaxation. The microscopic origin of the glass transition is a low-dimensional, slow manifold consisting largely of the Euler angles describing interhelical reorientation. Principal component analysis over a range of temperatures covering the glass transition shows that the abrupt slowdown of motion finds its explanation in a localization transition that traps probability density into several disconnected conformational pools over the low-dimensional energy landscape. Upon temperature increase, the probability density pools then flood a larger basin, akin to a lakes-to-sea transition. Simulations on transactivation response RNA are also used to backcalculate inelastic neutron scattering data that match previous inelastic neutron scattering measurements on larger and more complex RNA structures and which, upon normalization, give temperature-dependent fluctuation profiles that overlap onto a glass transition curve that is quasi-universal over a range of systems and techniques.
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Affiliation(s)
- Aaron T Frank
- Department of Chemistry, University of California at Irvine, Irvine, California
| | - Qi Zhang
- The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina
| | - Ioan Andricioaei
- Department of Chemistry, University of California at Irvine, Irvine, California.
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27
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Mallamace F, Corsaro C, Mallamace D, Vasi S, Vasi C, Stanley HE. Thermodynamic properties of bulk and confined water. J Chem Phys 2015; 141:18C504. [PMID: 25399169 DOI: 10.1063/1.4895548] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The thermodynamic response functions of water display anomalous behaviors. We study these anomalous behaviors in bulk and confined water. We use nuclear magnetic resonance (NMR) to examine the configurational specific heat and the transport parameters in both the thermal stable and the metastable supercooled phases. The data we obtain suggest that there is a behavior common to both phases: that the dynamics of water exhibit two singular temperatures belonging to the supercooled and the stable phase, respectively. One is the dynamic fragile-to-strong crossover temperature (T(L) ≃ 225 K). The second, T* ∼ 315 ± 5 K, is a special locus of the isothermal compressibility K(T)(T, P) and the thermal expansion coefficient α(P)(T, P) in the P-T plane. In the case of water confined inside a protein, we observe that these two temperatures mark, respectively, the onset of protein flexibility from its low temperature glass state (T(L)) and the onset of the unfolding process (T*).
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Affiliation(s)
- Francesco Mallamace
- Dipartimento di Fisica e Scienza della Terra Università di Messina and CNISM, I-98168 Messina, Italy
| | - Carmelo Corsaro
- Dipartimento di Fisica e Scienza della Terra Università di Messina and CNISM, I-98168 Messina, Italy
| | - Domenico Mallamace
- Dipartimento di Scienze dell'Ambiente, della Sicurezza, del Territorio, degli Alimenti e della Salute, Università di Messina, I-98166 Messina, Italy
| | | | | | - H Eugene Stanley
- Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215, USA
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28
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Petridis L, O’Neill HM, Johnsen M, Fan B, Schulz R, Mamontov E, Maranas J, Langan P, Smith JC. Hydration Control of the Mechanical and Dynamical Properties of Cellulose. Biomacromolecules 2014; 15:4152-9. [DOI: 10.1021/bm5011849] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | | | | | - Bingxin Fan
- Department
of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Roland Schulz
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | | | - Janna Maranas
- Department
of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Paul Langan
- Department
of Chemistry, University of Toledo, Toledo, Ohio 43606, United States
| | - Jeremy C. Smith
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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29
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Mallamace F, Baglioni P, Corsaro C, Chen SH, Mallamace D, Vasi C, Stanley HE. The influence of water on protein properties. J Chem Phys 2014; 141:165104. [DOI: 10.1063/1.4900500] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Francesco Mallamace
- Dipartimento di Fisica e Scienze della Terra, Universit à di Messina, I-98166, Messina, Italy
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215, USA
- Consiglio Nazionale delle Ricerche-IPCF, I-98166, Messina, Italy
| | - Piero Baglioni
- Dipartimento di Chimica and CSGI, Università di Firenze, 50019 Firenze, Italy
| | - Carmelo Corsaro
- Dipartimento di Fisica e Scienze della Terra, Universit à di Messina, I-98166, Messina, Italy
| | - Sow-Hsin Chen
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Domenico Mallamace
- Dipartimento di Scienze dell’Ambiente, della Sicurezza, del Territorio, degli Alimenti e della Salute, Università di Messina Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Cirino Vasi
- Consiglio Nazionale delle Ricerche-IPCF, I-98166, Messina, Italy
| | - H. Eugene Stanley
- Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215, USA
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30
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Konov KB, Isaev NP, Dzuba SA. Low-Temperature Molecular Motions in Lipid Bilayers in the Presence of Sugars: Insights into Cryoprotective Mechanisms. J Phys Chem B 2014; 118:12478-85. [DOI: 10.1021/jp508312n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Konstantin B. Konov
- Zavoisky
Physical-Technical Institute, Russian Academy of Sciences, Kazan 420029, Russia
| | - Nikolay P. Isaev
- Voevodsky
Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Sergei A. Dzuba
- Voevodsky
Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
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31
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Yoon J, Lin JC, Hyeon C, Thirumalai D. Dynamical Transition and Heterogeneous Hydration Dynamics in RNA. J Phys Chem B 2014; 118:7910-9. [DOI: 10.1021/jp500643u] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jeseong Yoon
- Korea Institute for Advanced Study, 130-722 Seoul, Korea
| | - Jong-Chin Lin
- Department
of Chemistry and Biochemistry, and Biophysics
Program, Institute for Physical Sciences and Technology, University of Maryland, College
Park, Maryland 20742, United States
| | | | - D. Thirumalai
- Department
of Chemistry and Biochemistry, and Biophysics
Program, Institute for Physical Sciences and Technology, University of Maryland, College
Park, Maryland 20742, United States
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32
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Schirò G, Vetri V, Andersen C, Natali F, Koza M, Leone M, Cupane A. The Boson Peak of Amyloid Fibrils: Probing the Softness of Protein Aggregates by Inelastic Neutron Scattering. J Phys Chem B 2014; 118:2913-23. [DOI: 10.1021/jp412277y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- G. Schirò
- Dipartimento
di Fisica e Chimica, Università di Palermo, 90136 Palermo, Italy
| | - V. Vetri
- Dipartimento
di Fisica e Chimica, Università di Palermo, 90136 Palermo, Italy
| | - C.B. Andersen
- Department
of Diabetes Biophysics, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | - F. Natali
- CNR-IOM, c/o Institut Laue Langevin, Grenoble, France
| | - M.M. Koza
- Institut Laue Langevin, Grenoble, France
| | - M. Leone
- Dipartimento
di Fisica e Chimica, Università di Palermo, 90136 Palermo, Italy
| | - A. Cupane
- Dipartimento
di Fisica e Chimica, Università di Palermo, 90136 Palermo, Italy
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33
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Dao TD, Hafez ME, Beloborodov I, Jeong HD. Thioacetic-Acid Capped PbS Quantum Dot Solids Exhibiting Thermally Activated Charge Hopping Transport. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.2.457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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34
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Abstract
Conformational changes in nucleic acids play a key role in the way genetic information is stored, transferred, and processed in living cells. Here, we describe new approaches that employ a broad range of experimental data, including NMR-derived chemical shifts and residual dipolar couplings, small-angle X-ray scattering, and computational approaches such as molecular dynamics simulations to determine ensembles of DNA and RNA at atomic resolution. We review the complementary information that can be obtained from diverse sets of data and the various methods that have been developed to combine these data with computational methods to construct ensembles and assess their uncertainty. We conclude by surveying RNA and DNA ensembles determined using these methods, highlighting the unique physical and functional insights obtained so far.
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Affiliation(s)
- Loïc Salmon
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109;
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35
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Ankner JF, Heller WT, Herwig KW, Meilleur F, Myles DAA. Neutron scattering techniques and applications in structural biology. ACTA ACUST UNITED AC 2013; Chapter 17:Unit17.16. [PMID: 23546619 DOI: 10.1002/0471140864.ps1716s72] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neutron scattering is exquisitely sensitive to the position, concentration, and dynamics of hydrogen atoms in materials and is a powerful tool for the characterization of structure-function and interfacial relationships in biological systems. Modern neutron scattering facilities offer access to a sophisticated, nondestructive suite of instruments for biophysical characterization that provides spatial and dynamic information spanning from Ångstroms to microns and from picoseconds to microseconds, respectively. Applications in structural biology range from the atomic-resolution analysis of individual hydrogen atoms in enzymes through to meso- and macro-scale analysis of complex biological structures, membranes, and assemblies. The large difference in neutron scattering length between hydrogen and deuterium allows contrast variation experiments to be performed and enables H/D isotopic labeling to be used for selective and systematic analysis of the local structure, dynamics, and interactions of multi-component systems. This overview describes the available techniques and summarizes their practical application to the study of biomolecular systems.
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Affiliation(s)
- John F Ankner
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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36
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Ngai KL, Capaccioli S, Paciaroni A. Change of caged dynamics at Tg in hydrated proteins: Trend of mean squared displacements after correcting for the methyl-group rotation contribution. J Chem Phys 2013; 138:235102. [DOI: 10.1063/1.4810752] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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37
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Chu XQ, Mamontov E, O'Neill H, Zhang Q. Temperature Dependence of Logarithmic-like Relaxational Dynamics of Hydrated tRNA. J Phys Chem Lett 2013; 4:936-942. [PMID: 26291359 DOI: 10.1021/jz400128u] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The dynamics of RNA within the β-relaxation region of 10 ps to 1 ns is crucial to its biological function. Because of its simpler chemical building blocks and the lack of the side methyl groups, faster relaxational dynamics of RNA compared to proteins can be expected. However, the situation is actually opposite. In this work, the relaxational dynamics of tRNA is measured by quasielastic neutron scattering and analyzed using the mode coupling theory, originally developed for glass-forming liquids. Our results reveal that the dynamics of tRNA follows a log-decay within the β-relaxation region, which is an important trait demonstrated by the dynamics of proteins. The dynamics of hydrated tRNA and lysozyme compared in the time domain further demonstrate that the slower dynamics of tRNA relative to proteins originates from the difference in the folded states of tRNA and proteins, as well as the influence of their hydration water.
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Affiliation(s)
- Xiang-Qiang Chu
- †Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
- ‡Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Eugene Mamontov
- §Chemical and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hugh O'Neill
- ‡Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Qiu Zhang
- ‡Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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38
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Lü X, Hu N, Li J, Ma H, Du K, Zhao R. Influence of TiO2 impregnated with a novel copper(II) carboxylic porphyrin and its application in photocatalytic degradation of 4-Nitrophenol. RESEARCH ON CHEMICAL INTERMEDIATES 2013. [DOI: 10.1007/s11164-013-1089-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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Giel-Pietraszuk M, Barciszewski J. Hydrostatic and osmotic pressure study of the RNA hydration. Mol Biol Rep 2012; 39:6309-18. [PMID: 22314910 PMCID: PMC3310992 DOI: 10.1007/s11033-012-1452-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 01/23/2012] [Indexed: 11/17/2022]
Abstract
The tertiary structure of nucleic acids results from an equilibrium between electrostatic interactions of phosphates, stacking interactions of bases, hydrogen bonds between polar atoms and water molecules. Water interactions with ribonucleic acid play a key role in its structure formation, stabilization and dynamics. We used high hydrostatic pressure and osmotic pressure to analyze changes in RNA hydration. We analyzed the lead catalyzed hydrolysis of tRNAPhe from S. cerevisiae as well as hydrolytic activity of leadzyme. Pb(II) induced hydrolysis of the single phosphodiester bond in tRNAPhe is accompanied by release of 98 water molecules, while other molecule, leadzyme releases 86.
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Affiliation(s)
- Małgorzata Giel-Pietraszuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
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40
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Role of methyl groups in dynamics and evolution of biomolecules. J Biol Phys 2012; 38:497-505. [PMID: 23729910 DOI: 10.1007/s10867-012-9268-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 03/19/2012] [Indexed: 10/28/2022] Open
Abstract
Recent studies have discovered strong differences between the dynamics of nucleic acids (RNA and DNA) and proteins, especially at low hydration and low temperatures. This difference is caused primarily by dynamics of methyl groups that are abundant in proteins, but are absent or very rare in RNA and DNA. In this paper, we present a hypothesis regarding the role of methyl groups as intrinsic plasticizers in proteins and their evolutionary selection to facilitate protein dynamics and activity. We demonstrate the profound effect methyl groups have on protein dynamics relative to nucleic acid dynamics, and note the apparent correlation of methyl group content in protein classes and their need for molecular flexibility. Moreover, we note the fastest methyl groups of some enzymes appear around dynamical centers such as hinges or active sites. Methyl groups are also of tremendous importance from a hydrophobicity/folding/entropy perspective. These significant roles, however, complement our hypothesis rather than preclude the recognition of methyl groups in the dynamics and evolution of biomolecules.Electronic supplementary material The online version of this article (doi:10.1007/s10867-012-9268-6) contains supplementary material, which is available to authorized users.
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41
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42
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Linden AH, Franks WT, Akbey Ü, Lange S, van Rossum BJ, Oschkinat H. Cryogenic temperature effects and resolution upon slow cooling of protein preparations in solid state NMR. JOURNAL OF BIOMOLECULAR NMR 2011; 51:283-92. [PMID: 21826519 DOI: 10.1007/s10858-011-9535-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 07/18/2011] [Indexed: 05/09/2023]
Abstract
X-ray crystallography using synchrotron radiation and the technique of dynamic nuclear polarization (DNP) in nuclear magnetic resonance (NMR) require samples to be kept at temperatures below 100 K. Protein dynamics are poorly understood below the freezing point of water and down to liquid nitrogen temperatures. Therefore, we investigate the α-spectrin SH3 domain by magic angle spinning (MAS) solid state NMR (ssNMR) at various temperatures while cooling slowly. Cooling down to 95 K, the NMR-signals of SH3 first broaden and at lower temperatures they separate into several peaks. The coalescence temperature differs depending on the individual residue. The broadening is shown to be inhomogeneous by hole-burning experiments. The coalescence behavior of 26 resolved signals (of 62) was compared to water proximity and crystal structure Debye-Waller factors (B-factors). Close proximity to the solvent and large B-factors (i.e. mobility) lead, generally, to a higher coalescence temperature. We interpret a high coalescence temperature as indicative of a large number of magnetically inequivalent populations at cryogenic temperature.
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Affiliation(s)
- Arne H Linden
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
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43
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Matyushov DV, Morozov AY. Electrostatics of the protein-water interface and the dynamical transition in proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:011908. [PMID: 21867214 DOI: 10.1103/physreve.84.011908] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2010] [Indexed: 05/31/2023]
Abstract
Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent experiments indicate a connection between the dynamical transition and the dielectric response of the hydrated protein. We analyze two mechanisms of the coupling between the protein atomic motions and the protein-water interface. The first mechanism considers viscoelastic changes in the global shape of the protein plasticized by its coupling to the hydration shell. The second mechanism involves modulations of the local motions of partial charges inside the protein by electrostatic fluctuations. The model is used to analyze mean-square displacements of iron of metmyoglobin reported by Mössbauer spectroscopy. We show that high displacement of heme iron at physiological temperatures is dominated by electrostatic fluctuations. Two onsets, one arising from the viscoelastic response and the second from electrostatic fluctuations, are seen in the temperature dependence of the mean-square displacements when the corresponding relaxation times enter the instrumental resolution window.
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Affiliation(s)
- Dmitry V Matyushov
- Center for Biological Physics, Arizona State University, PO Box 871604, Tempe, AZ 85287-1604, USA.
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44
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Khodadadi S, Roh JH, Kisliuk A, Mamontov E, Tyagi M, Woodson SA, Briber RM, Sokolov AP. Dynamics of biological macromolecules: not a simple slaving by hydration water. Biophys J 2010; 98:1321-6. [PMID: 20371332 DOI: 10.1016/j.bpj.2009.12.4284] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 11/24/2009] [Accepted: 12/04/2009] [Indexed: 11/29/2022] Open
Abstract
We studied the dynamics of hydrated tRNA using neutron and dielectric spectroscopy techniques. A comparison of our results with earlier data reveals that the dynamics of hydrated tRNA is slower and varies more strongly with temperature than the dynamics of hydrated proteins. At the same time, tRNA appears to have faster dynamics than DNA. We demonstrate that a similar difference appears in the dynamics of hydration water for these biomolecules. The results and analysis contradict the traditional view of slaved dynamics, which assumes that the dynamics of biological macromolecules just follows the dynamics of hydration water. Our results demonstrate that the dynamics of biological macromolecules and their hydration water depends strongly on the chemical and three-dimensional structures of the biomolecules. We conclude that the whole concept of slaving dynamics should be reconsidered, and that the mutual influence of biomolecules and their hydration water must be taken into account.
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Affiliation(s)
- S Khodadadi
- Department of Polymer Science, University of Akron, Akron, Ohio, USA
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45
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Nikolova EN, Al-Hashimi HM. Thermodynamics of RNA melting, one base pair at a time. RNA (NEW YORK, N.Y.) 2010; 16:1687-1691. [PMID: 20660079 PMCID: PMC2924531 DOI: 10.1261/rna.2235010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The melting of base pairs is a ubiquitous feature of RNA structural transitions, which are widely used to sense and respond to cellular stimuli. A recent study employing solution nuclear magnetic resonance (NMR) imino proton exchange spectroscopy provides a rare base-pair-specific view of duplex melting in the Salmonella FourU RNA thermosensor, which regulates gene expression in response to changes in temperature at the translational level by undergoing a melting transition. The authors observe "microscopic" enthalpy-entropy compensation--often seen "macroscopically" across a series of related molecular species--across base pairs within the same RNA. This yields variations in base-pair stabilities that are an order of magnitude smaller than corresponding variations in enthalpy and entropy. A surprising yet convincing link is established between the slopes of enthalpy-entropy correlations and RNA melting points determined by circular dichroism (CD), which argues that unfolding occurs when base-pair stabilities are equalized. A single AG-to-CG mutation, which enhances the macroscopic hairpin thermostability and folding cooperativity and renders the RNA thermometer inactive in vivo, spreads its effect microscopically throughout all base pairs in the RNA, including ones far removed from the site of mutation. The authors suggest that an extended network of hydration underlies this long-range communication. This study suggests that the deconstruction of macroscopic RNA unfolding in terms of microscopic unfolding events will require careful consideration of water interactions.
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Affiliation(s)
- Evgenia N Nikolova
- Chemical Biology Doctoral Program, Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
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46
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Kobus M, Nguyen PH, Stock G. Infrared signatures of the peptide dynamical transition: A molecular dynamics simulation study. J Chem Phys 2010; 133:034512. [DOI: 10.1063/1.3462961] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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47
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LeBard DN, Matyushov DV. Ferroelectric Hydration Shells around Proteins: Electrostatics of the Protein−Water Interface. J Phys Chem B 2010; 114:9246-58. [DOI: 10.1021/jp1006999] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- David N. LeBard
- Center for Biological Physics, Arizona State University, PO Box 871604, Tempe, Arizona 85287-1604
| | - Dmitry V. Matyushov
- Center for Biological Physics, Arizona State University, PO Box 871604, Tempe, Arizona 85287-1604
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48
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Zuo G, Wang J, Qin M, Xue B, Wang W. Effect of solvation-related interaction on the low-temperature dynamics of proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:031917. [PMID: 20365780 DOI: 10.1103/physreve.81.031917] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Revised: 12/06/2009] [Indexed: 05/29/2023]
Abstract
The effect of solvation-related interaction on the low-temperature dynamics of proteins is studied by taking into account the desolvation barriers in the interactions of native contacts. It is found out that about the folding transition temperature, the protein folds in a cooperative manner, and the water molecules are expelled from the hydrophobic core at the final stage in the folding process. At low temperature, however, the protein would generally be trapped in many metastable conformations with some water molecules frozen inside the protein. The desolvation takes an important role in these processes. The number of frozen water molecules and that of frozen states of proteins are further analyzed with the methods based on principal component analysis (PCA) and the clustering of conformations. It is found out that both the numbers of frozen water molecules and the frozen states of the protein increase quickly below a certain temperature. Especially, the number of frozen states of the protein increases exponentially following the decrease in the temperature, which resembles the basic features of glassy dynamics. Interestingly, it is observed that the freezing of water molecules and that of protein conformations happen at almost the same temperature. This suggests that the solvation-related interaction performs an important role for the low-temperature dynamics of the model protein.
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Affiliation(s)
- Guanghong Zuo
- Nanjing National Laboratory of Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
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Mamontov E, O'Neill H, Zhang Q. Mean-squared atomic displacements in hydrated lysozyme, native and denatured. J Biol Phys 2010; 36:291-7. [PMID: 21629590 DOI: 10.1007/s10867-009-9184-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 12/22/2009] [Indexed: 10/20/2022] Open
Abstract
We use elastic neutron scattering to demonstrate that a sharp increase in the mean-squared atomic displacements, commonly observed in hydrated proteins above 200 K and often referred to as the dynamical transition, is present in the hydrated state of both native and denatured lysozyme. A direct comparison of the native and denatured protein thus confirms that the presence of the transition in the mean-squared atomic displacements is not specific to biologically functional molecules.
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Khodadadi S, Malkovskiy A, Kisliuk A, Sokolov A. A broad glass transition in hydrated proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:15-9. [DOI: 10.1016/j.bbapap.2009.05.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 04/16/2009] [Accepted: 05/29/2009] [Indexed: 11/28/2022]
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